SAS Clinical Standards Toolkit 1.5 Operational Qualification

SAS Clinical Standards Toolkit 1.5 Operational Qualification
SAS Clinical Standards
Toolkit 1.5
®
Operational Qualification
SAS® Documentation
The correct bibliographic citation for this manual is as follows: SAS Institute Inc. 2013. SAS® Clinical Standards Toolkit 1.5:
Operational Qualification. Cary, NC: SAS Institute Inc.
SAS® Clinical Standards Toolkit 1.5: Operational Qualification
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Contents
PART 1
Before You Begin
1
Chapter 1 / Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Purpose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Assumptions and Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
The Standards in This Document . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
PART 2
Internal Validation
9
Chapter 2 / Installation Qualification and Operational Qualification . . . . . . . . . . . . . . . 11
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
PART 3
ODM 19
Chapter 3 / Test 1: Create SAS ODM from XML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Chapter 4 / Test 2: Validate SAS ODM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
iv Contents
Chapter 5 / Test 3: Create ODM XML from SAS ODM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Chapter 6 / Test 4: Find Unsupported Tags in ODM XML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
PART 4
CRT-DDS
37
Chapter 7 / Test 1: Validate CRT-DDS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Chapter 8 / Test 2: Create SAS CRT-DDS from SDTM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Chapter 9 / Test 3: Create SAS CRT-DDS from Define.xml . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Chapter 10 / Test 4: Import from XML, Export to XML (Round Trip) . . . . . . . . . . . . . . . . 51
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Chapter 11 / Test 5: Create Define.xml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Contents
v
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
PART 5
SDTM 59
Chapter 12 / Test 1: Validate SDTM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Chapter 13 / Test 2: Build Source Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Chapter 14 / Test 3: Build Source Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Chapter 15 / Test 4: Build SAS Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Chapter 16 / Test 5: Report Check Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
vi Contents
1
Part 1
Before You Begin
Chapter 1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2
3
1
Introduction
Purpose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Assumptions and Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
General Assumptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
File Path Separator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
SASINSTALL and SASROOT within This Document . . . . . . . . . . . . . . . 5
Variables Referred to by the Tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Generation of a PDF File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
The Standards in This Document . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Purpose
Starting with the SAS Clinical Standards Toolkit 1.5, an internal validation process is
provided. This process has been designed using tools and metadata already available
with the product. In other words, the SAS Clinical Standards Toolkit is set up as a
standard within the product and is validated against a set of reference metadata.
The SAS Clinical Standards Toolkit internal validation addresses two primary use
cases:
n
Perform installation qualification and operational qualification.
This is implemented with and illustrated by the use of the validate_iqoq sample
driver, located in the sample study library directory/cstframework-1.5/programs folder. This is a two-step process.
4 Chapter 1 / Introduction
1 Select the CST-FRAMEWORK standard, and run the checks that are defined in
the validation_control_glmeta view of the internal validation validation_master
data set. This is a set of 64 checks (checkid < CSTV100) that look only at the
global standards library metadata folder.
2 Select 1 to n specific standards, and run the checks that are defined in the
validation_control_stdiqoq view of the internal validation validation_master data
set. This is a set of 30 checks (checkid > CSTV100 that are relevant to
installation qualification and operational qualification issues) that look only at
metadata libraries other than the global standards library metadata folder.
n
Perform validation on standard-specific metadata.
This is implemented with and illustrated by the use of the validate_standard sample
driver. Select 1 to n specific standards, and run the checks that are defined in the
validation_control_std view of the internal validation validation_master data set.
This is a set of 39 checks (checkid > CSTV100) that look only at metadata libraries
other than the global standards library metadata folder.
For the purpose of operational qualification, this document implements the SAS Clinical
Standards Toolkit internal validation for installation qualification and operational
qualification.
For more information about internal validation, see Chapter 7, “Internal Validation,” in
the SAS Clinical Standards Toolkit: User’s Guide.
This document explains how to verify that the SAS Clinical Standards Toolkit 1.5 has
been installed correctly and is operating properly. The installation is tested by running a
series of SAS Clinical Standards Toolkit internal validation programs. These programs
must be run in the sequence that they are presented. In addition to the internal
validation process, a separate process enables you to manually run driver programs to
verify that the product is operating correctly.
Assumptions and Notes
5
Assumptions and Notes
General Assumptions
n
The second maintenance release for SAS 9.3 has been installed and is functioning
correctly. It is not being tested.
n
The SAS Clinical Standards Toolkit 1.5 has been installed, including the sample
study libraries.
n
The person running these tests is familiar with running SAS programs. This includes
being able to submit SAS programs via the Program Editor, review the SAS log, and
review the contents of SAS data sets.
File Path Separator
This document is used for both the UNIX and Microsoft Windows environments. The
forward slash character ( / ) is used in file paths as the separator between path
components, which works in both operating system environments.
SASINSTALL and SASROOT within This
Document
n
SASINSTALL is used to denote the SAS installation directory. This is the directory
into which all SAS products are installed.
The default value in SAS 9.3 on Microsoft Windows is C:/Program Files/
SASHome.
The default value varies on UNIX computers. Please consult your system
administrator.
n
SASROOT is used to denote the root directory for the SAS System installation.
The default value in SAS 9.3 is SASINSTALL/SASFoundation/9.3.
6 Chapter 1 / Introduction
n
sample study library directory is used to denote the sample study libraries available
with the SAS Clinical Standards Toolkit 1.5.
The default value for the SAS Clinical Standards Toolkit 1.5 on Microsoft Windows is
C:/cstSampleLibrary.
Variables Referred to by the Tests
The tests refer to the following variables, which are defined relative to sample study
library directory. When running the tests, substitute the variables with these associated
paths:
n
CST_FRAMEWORK
sample study library directory/cdisc-sdtm-3.1.1–1.5/
sascstdemodata
n
CST_SDTM
sample study library directory/cdisc-sdtm-3.1.2–1.5/
sascstdemodata
n
CST_ODM_130
sample study library directory/cdisc-odm-1.3.0–1.5
n
CST_ODM
sample study library directory/cdisc-odm-1.3.1–1.5
n
CST_CRTDDS
sample study library directory/cdisc-crtdds-1.0–1.5
Generation of a PDF File
The last manual test (see Chapter 16, “Test 5: Report Check Metadata,” on page 79)
generates a PDF file. On Microsoft Windows, when a PDF file is generated, the PDF
should automatically appear in a browser window. On UNIX, if you have not set up the
SAS configuration variable SAS.helpBrowser, you see this message:
The Standards in This Document
7
The requested information could not be displayed because the
connection to the remote browser server failed.
Click OK to continue.
Configure your UNIX SAS environment to support a browser that can display PDF files.
Or, copy the PDF file to an environment where you can display it.
The Standards in This Document
The parts in this document that describe the standards are samples of several
standards from the SAS Clinical Standards Toolkit. Each part describes how to access
the sample study data using the driver programs to verify that the data, the metadata,
and the SAS Clinical Standards Toolkit macros are functioning properly.
8 Chapter 1 / Introduction
9
Part 2
Internal Validation
Chapter 2
Installation Qualification and Operational Qualification . . . . . 11
10
11
2
Installation Qualification and
Operational Qualification
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Introduction
Installation qualification and operational qualification is implemented with and illustrated
by the use of the validate_iqoq sample driver, located in the sample study library
directory/cst-framework-1.5/programs folder. This is a two-step process.
1 Select the CST-FRAMEWORK standard, and run the checks that are defined in the
validation_control_glmeta view of the internal validation validation_master data set.
This is a set of 64 checks (checkid < CSTV100) that look only at the global
standards library metadata folder.
2 Select 1 to n specific standards, and run the checks that are defined in the
validation_control_stdiqoq view of the internal validation validation_master data set.
This is a set of 30 checks (checkid > CSTV100 that are relevant to installation
qualification and operational qualification issues) that look only at the metadata
libraries other than the global standards library metadata folder.
12 Chapter 2 / Installation Qualification and Operational Qualification
Note: The validation Results data set that is generated by the internal validation
installation qualification and operational qualification contains many observations. Your
number of observations can differ from the numbers shown in this document due to
installation configurations that differ from a default installation of the SAS Clinical
Standards Toolkit. For example, CDSIC SEND might not be installed.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_FRAMEWORK/programs/validate_iqoq.sas.
3 Select Run  Submit.
The program outputs to the SAS log and creates a cstrslt.validation_results data set
under CST_FRAMEWORK/results.
Note: The SAS log might reach its limit depending on your system options. If it
does, print the contents to a file, and select APPEND in the pop-up menu. This can
happen several times during the run, so be sure to append each time it happens. To
maximize the log size, you can add the option –DMSLOGSIZE 999999 to the SAS
configuration file.
4 If the SAS log reaches it limit, perform these steps:
a In the pop-up window, select F to file.
Steps 13
b Enter a filename, and select APPEND or REPLACE.
Note: Select REPLACE for the first occurrence of the pop-up window only.
c Click END.
d Repeat steps a through c until finished.
Use the same filename each time, and select APPEND.
5 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
6 The column labeled Process status (named _cst_rc) is 0 for all records.
7 Review the cstrslt.validation_results data set using the SAS explorer, especially for
the following conditions:
a The field resultflag is not 0.
When this value is not 0, a potential problem might exist. To more easily check
this value, subset the validation_results data set by entering where
resultflag ne 0 in the control box in the upper left:
14 Chapter 2 / Installation Qualification and Operational Qualification
b A number of observations can have result flag=1.
If the resultseverity column is Note, these values are acceptable. To more
easily check these values, subset the validation_results data set by entering
where resultflag = "Note" (this is case sensitive) in the control box in the
upper left:
Here are examples of where resultseverity="Note" and resultflag ne 0:
n
In this example, multiple records are detected because there are multiple
standard versions for ODM (1.3.0 and 1.3.1) and SDTM (3.1.1, 3.1.2, and
3.1.3). If multiple records were found for the same standard version, this
check would be in error.
n
In this example, a check was not run because the check is not applicable to
this standard. An informational check informs you that check CSTV251 is not
applicable to this standard.
Steps 15
n
In this example, a check was not run because the check has not yet been
implemented in the SAS Clinical Standards Toolkit. Check CSTV262 included
with the SAS Clinical Standards Toolkit has not yet been implemented in this
release. Therefore, the check did not run.
n
In this example, these data sets are empty. They are empty because they are
templates and do not contain observations.
n
In this example, resultseverity equals Info because the controlled
terminology does not have an sl_cntl folder associated with it. There are no
control type data sets associated with controlled terminology.
No observations should appear when you enter where resultseverity =
"Error" in the control box in the upper left.
8 Close the SAS session.
16 Chapter 2 / Installation Qualification and Operational Qualification
Running the validate_iqoq internal validation program without error confirms that all
metadata is in place, all files are in place, and all access (whether Read or Write) to the
SAS Clinical Standards Toolkit is properly initialized. This process has ensured that the
installation of the SAS Clinical Standards Toolkit was done properly and that the key
components are operational.
Sign-Off 17
Sign-Off
Internal Validation - Installation Qualification and Operational Qualification
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
18 Chapter 2 / Installation Qualification and Operational Qualification
19
Part 3
ODM
Chapter 3
Test 1: Create SAS ODM from XML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Chapter 4
Test 2: Validate SAS ODM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Chapter 5
Test 3: Create ODM XML from SAS ODM . . . . . . . . . . . . . . . . . . . . . . . 29
Chapter 6
Test 4: Find Unsupported Tags in ODM XML . . . . . . . . . . . . . . . . . . 33
20
21
3
Test 1: Create SAS ODM from XML
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Introduction
This test reads a CDISC ODM 1.3.0 XML file and builds a SAS representation of the
metadata that is defined in the XML.
Note: To run against ODM 1.3.0, use the same information in this section, but
substitute 1.3.1 with 1.3.0. Running against ODM 1.3.0 creates fewer data sets and less
content (rows) within data sets.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_ODM/Programs/create_sasodm_fromxml.sas.
3 Select Run  Submit.
22 Chapter 3 / Test 1: Create SAS ODM from XML
This program outputs to the SAS log and creates data sets in the formats, metadata,
and data subdirectories in the CST_ODM/derived directory. It also creates a
read_results data set in the CST_ODM/results directory.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the read_results data set in the CST_ODM/results directory to ensure that
the following conditions are met:
TIP In the SAS Explorer, you can view it as Read_results in the Results library.
n
The message column contains correct paths and process metadata.
n
The column labeled Process status (named _cst_rc) is 0 for all records.
n
The data set contains 54 records (for ODM 1.3.1).
n
Row 53 reports that the ODM file was read successfully.
6 Review the CST_ODM/derived/metadata directory to ensure that the following
conditions are met:
TIP In the SAS Explorer, you can view these data sets in the Srcmetalibrary.
n
The directory contains two data sets: source_tables and source_columns.
n
The source_tables data set contains 76 rows and 10 columns.
n
The source_columns data set contains 352 rows and 16 columns.
7 Review the CST_ODM/derived/data directory to ensure that the following
conditions are met:
n
There are 76 new SAS data sets. (Do not count any data sets that are not SAS,
such as .xpt files.)
n
The codelists data set contains 23 records and five columns.
Sign-Off 23
8 Review the CST_ODM/derived/formats directory to ensure that the following
conditions are met:
n
There are three new SAS data sets and three new SAS format catalogs. (Do not
count any data sets that are not SAS, such as .xpt files.)
n
The odmfmtcat_en data set contains 957 records and five columns.
9 Close the SAS session.
Sign-Off
Test 1: Create SAS ODM from XML
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
24 Chapter 3 / Test 1: Create SAS ODM from XML
25
4
Test 2: Validate SAS ODM
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Introduction
This test validates a SAS representation of the metadata that is defined in the CDISC
ODM 1.3.1 XML file.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_ODM/Programs/validate_odm_data.sas.
3 Select Run  Submit.
The program outputs to the SAS log and creates a validation_results data set and a
validation_metrics data set in the CST_ODM/results directory.
26 Chapter 4 / Test 2: Validate SAS ODM
Note: This program can fill up the log window if running interactively. If so, save the
output of the log to a file when prompted to do so.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the validation_results data set in the CST_ODM/results directory to ensure
that the following conditions are met:
TIP In the SAS Explorer, you can view it as validation_results in the Results
library.
n
The column labeled Process status (named _cst_rc) is 0 for all records. There
are two failures of ODM0110.
n
The data set contains 385 records.
n
There are two records with resultflag=1 and resultseverity="Error". Both
of these records have checkid="ODM0110".
Note: The errors messages are expected and are included in the sample data to
cause a validation error for demonstration purposes.
6 Review the validation_metrics data set in the CST_ODM/results directory to
ensure that the following conditions are met:
TIP In the SAS Explorer, you can view it as validation_metrics in the Results
library.
n
The data set contains 656 records.
n
The last record reports that there were two records with "Content errors,
warnings and notes".
7 Close the SAS session.
Sign-Off 27
Sign-Off
Test 2: Validate SAS ODM
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
28 Chapter 4 / Test 2: Validate SAS ODM
29
5
Test 3: Create ODM XML from SAS
ODM
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Introduction
This test creates a CDISC ODM 1.3.1 XML file from the SAS representation of the
metadata.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_ODM/Programs/create_odmxml.sas.
3 Select Run  Submit.
30 Chapter 5 / Test 3: Create ODM XML from SAS ODM
The program outputs to the SAS log, creates an XML file odm_sample_out.xml in
the CST_ODM/sourcexml directory. It also creates a write_results data set in the
CST_ODM/results directory.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the write_results data set in the CST_ODM/results directory to ensure that
the following conditions are met:
TIP In the SAS Explorer, you can also view it as Write_results in the Results
library.
n
The column labeled Process status (named _cst_rc) is 0 for all records.
n
The column named resultflag is 0 for all records.
n
The data set contains 70 records.
n
There is a record that contains scrdata="ODM_WRITE" that reports that the ODM
file was created.
n
The last record that contains srcdata="ODM_XMLVALIDATE" reports that no errors
were found in the ODM file.
6 Ensure that the CST_ODM/sourcexml directory contains a new XML file
odm_sample_out.xml that has the same size (321 KB) as the XML file
odm_sample.xml in the same directory.
7 Close the SAS session.
Sign-Off 31
Sign-Off
Test 3: Create ODM XML from SAS ODM
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
32 Chapter 5 / Test 3: Create ODM XML from SAS ODM
33
6
Test 4: Find Unsupported Tags in ODM
XML
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Introduction
This test parses a CDISC ODM 1.3.1 XML file and finds elements and attributes that the
SAS Clinical Standards Toolkit does not recognize by default. These elements and
attributes might be vendor extensions, customer extensions, or new tags implemented
in a later version of ODM.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_ODM/Programs/find_unsupported_tags.sas.
3 Select Run  Submit.
34 Chapter 6 / Test 4: Find Unsupported Tags in ODM XML
The program outputs to the SAS log and creates a readxmltags_results data set in
the CST_ODM/results directory.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the readxmltags _results data set in the CST_ODM/results directory to
ensure that the following conditions are met:
TIP In the SAS Explorer, you can view it as readxmltags_results in the Results
library.
n
The column labeled Process status (named _cst_rc) is 0 for all records.
n
The column named resultflag is 0 for eight records, and 1 for all other records.
n
The data set contains 28 records.
n
There are four records that contain checkid="ODM0900" and 16 records that
contain checkid="ODM0901". For the ODM0900 check, the message indicates
"Element found in XML file that is not present in CDISC ODM Model".
For the ODM0901 check, the message indicates "Attribute found in XML
file that is not present in CDISC ODM Model".
6 Close the SAS session.
Sign-Off 35
Sign-Off
Test 4: Find Unsupported Tags in ODM XML
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
36 Chapter 6 / Test 4: Find Unsupported Tags in ODM XML
37
Part 4
CRT-DDS
Chapter 7
Test 1: Validate CRT-DDS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Chapter 8
Test 2: Create SAS CRT-DDS from SDTM . . . . . . . . . . . . . . . . . . . . . . . 43
Chapter 9
Test 3: Create SAS CRT-DDS from Define.xml . . . . . . . . . . . . . . . . . 47
Chapter 10
Test 4: Import from XML, Export to XML (Round Trip) . . . . . . . 51
Chapter 11
Test 5: Create Define.xml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
38
39
7
Test 1: Validate CRT-DDS
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Introduction
This test validates a SAS representation of the metadata and data that is defined in the
SAS representation of the CRT-DDS 1.0 model.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_CRTDDS/Programs/validate_crtdds_data.sas.
3 Select Run  Submit.
This program outputs to the SAS log and creates a validation_results data set and a
validation_metrics data set in the CST_CRTDDS/results directory.
40 Chapter 7 / Test 1: Validate CRT-DDS
Note: This code can fill up the log window if running interactively. If so, save the
output of the log to a file when prompted to do so.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the validation_results data set in the CST_CRTDDS/results directory to
ensure that the following conditions are met:
TIP In the SAS Explorer, you can view it as validation_results in the Results
library.
n
The column labeled Process status (named _cst_rc) is 0 for all records.
n
The data set contains 202 records.
n
There are 21 records that contain "Warning: Check not run." These records
contain checkid="CRT0100" and resultid="CST0022".
6 Review the validation_metrics data set in the CST_CRTDDS/results directory to
ensure that the following conditions are met:
TIP In the SAS Explorer, you can view it as validation_metrics in the Results
library.
n
The data set contains 326 records.
n
The last record reports that there were 21 records with "Content errors,
warnings and notes".
7 Close the SAS session.
Sign-Off 41
Sign-Off
Test 1: Validate CRT-DDS
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
42 Chapter 7 / Test 1: Validate CRT-DDS
43
8
Test 2: Create SAS CRT-DDS from
SDTM
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Introduction
If this program runs successfully and produces the expected results, the SAS Clinical
Standards Toolkit has derived CRT-DDS 1.0 metadata from an SDTM study as a
prerequisite to building a define.xml file in Test 5.
Steps
1 Start a new SAS session, and submit the sample program CST_CRTDDS/
programs/create_crtdds_from_sdtm.sas.
The sample program outputs to the SAS Log and creates 39 data sets in the
CST_CRTDDS/data directory and a Results data set in the CST_CRTDDS/results
directory.
2 Review the log to see whether there are any errors or warnings.
44 Chapter 8 / Test 2: Create SAS CRT-DDS from SDTM
There might be one warning when using the SAS Clinical Standards Toolkit sample
data:
WARNING: Multiple lengths were specified for the variable Role
by input data set(s). This may cause truncation of data.
3 Review the CST_CRTDDS/data directory to ensure that the following conditions are
met:
TIP In the SAS Explorer, you can view it in the srcdata library.
n
There are 39 new SAS data sets.
n
The codelists data set has 46 records and 5 columns.
4 Review the sdtmtodefine_results data set in the CST_CRTDDS/results directory to
ensure that the following conditions are met:
TIP In the SAS Explorer, you can view it as sdtmtodefine_results in the Results
library.
n
The column labeled Process status (named _cst_rc) is 0 for all records.
n
The data set contains 40 records.
5 Close the SAS session.
Sign-Off 45
Sign-Off
Test 2: Create SAS CRT-DDS from SDTM
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
46 Chapter 8 / Test 2: Create SAS CRT-DDS from SDTM
47
9
Test 3: Create SAS CRT-DDS from
Define.xml
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Introduction
This test creates a CRT-DDS 1.0 SAS representation file from the define.xml.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_CRTDDS/Programs/create_sascrtdds_fromxml.sas.
3 Select Run  Submit.
This program outputs to the SAS log and creates the SAS representation of the
CRT-DDS data sets in the CST_CRTDDS/deriveddata directory.
48 Chapter 9 / Test 3: Create SAS CRT-DDS from Define.xml
TIP In the SAS Explorer, you can also view it in the srcdata library.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the read_results data set in the CST_CRTDDS/results directory to ensure
that the following conditions are met:
TIP In the SAS Explorer, you can also view it as read_results in the Results
library.
n
The column labeled Process status (named _cst_rc) is 0 for all records.
n
The column named resultflag is 0 for all records.
n
The data set contains 50 records.
n
There is a record that contains scrdata="CRTDDS_READ" that reports that the
define.xml file was read successfully.
n
There is a record that contains srcdata="JAVA CHECK" that reports "No java
issues".
6 Ensure that the CST_CRTDDS/deriveddata directory contains 39 SAS data sets
that represent the SAS interpretation of the CRT-DDS format.
7 Open the clitemdecodetranslatedtext SAS data set.
It must contain 2909 observations. The first 17 observations are shown in this figure.
Steps 49
8 Close the SAS session.
50 Chapter 9 / Test 3: Create SAS CRT-DDS from Define.xml
Sign-Off
Test 3: Create SAS CRT-DDS from Define.xml
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
51
10
Test 4: Import from XML, Export to XML
(Round Trip)
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Introduction
This test reads a CRT-DDS define.xml file and creates the 39 SAS data sets in the
Work library representing the CRT-DDS 1.0 model. It then exports these generated data
sets and creates a CRT-DDS define.xml file. This verifies the round-tripping from XML
to data to XML.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_CRTDDS/Programs/import_sascrtdds_fromxml_export_toxml.sas.
3 Select Run  Submit.
52 Chapter 10 / Test 4: Import from XML, Export to XML (Round Trip)
This program outputs to the SAS log and creates a define1-0-0.xsl file and a
define_export.xml file in the CST_CRTDDS/sourcexml directory. It also creates a
import_results data set in the CST_CRTDDS/results directory.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 In the SAS Explorer, review the data in the Work directory to ensure that the
following conditions are met:
n
There are 39 data sets representing SAS interpretation of the CRT-DDS model.
n
These data sets do not contain any underscores in their names.
6 Review the import_results data set in the CST_CRTDDS/results directory to
ensure that the following conditions are met:
TIP In the SAS Explorer, you can view it as import_results in the Results
library.
n
The column labeled Process status (named _cst_rc) is 0 for all records.
n
The column named resultflag is 0 for all records.
n
The data set contains 47 records.
n
There is a record that contains scrdata="CRTDDS_READ" that reports that the
define_import.xml file was read successfully.
n
There is a record that contains srcdata="JAVA CHECK" that reports "No java
issues".
7 Review the export_results data set in the CST_CRTDDS/results directory to
ensure that the following conditions are met:
TIP In the SAS Explorer, you can view it as export_results in the Results library.
n
The column labeled Process status (named _cst_rc) is 0 for all records.
n
The column named resultflag is 0 for all records.
Steps 53
n
The data set contains 105 records.
n
There is a record that contains scrdata="CRTDDS_WRITE" that reports that the
define_export.xml file was created (row 82).
n
There is a record that contains srcdata="JAVA CHECK" that reports "No java
issues" (row 85).
8 In the CST_CRTDDS/sourcexml directory, ensure that the files define_import.xml
and define_export.xml are each 201 KB.
9 Double-click the define_export.xml file to open it, and click Vital Signs next to the
VS table.
The VS table appears.
10 Click the VSTESTCD variable.
11 Click the SIZE variable in the VSTESTCD–FRMSIZE row, and ensure that the table
looks like this:
12 Close the SAS session.
54 Chapter 10 / Test 4: Import from XML, Export to XML (Round Trip)
Sign-Off
Test 4: Import from XML, Export to XML (Round Trip)
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
55
11
Test 5: Create Define.xml
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Introduction
If this program runs successfully and produces the expected results, the SAS Clinical
Standards Toolkit Java and XML-related libraries have been installed correctly. The
SAS Clinical Standards Toolkit and libraries can create a CRT-DDS file (define.xml).
Steps
1 Start a new SAS session, and submit the sample program CST_CRTDDS/
programs/create_crtdds_define.sas.
This program writes to the SAS log and generates two files in CST_CRTDDS/
sourcexml directory and a Results data set in the CST_CRTDDS/results
directory.
2 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
56 Chapter 11 / Test 5: Create Define.xml
3 Ensure that two files were generated in the CST_CRTDDS/sourcexml directory:
define.xml and define1-0-0.xsl.
4 Open the define.xml file.
On Microsoft Windows, you can open it by double-clicking it in the SAS Program
Editor. This renders the file in your default web browser or any other application that
has been associated with XML files.
On UNIX, if you have not set up your browser configuration in SAS, you need to
copy define.xml and define1-0-0.xsl to an environment where you can display the
define.xml file in a web browser.
Note: The style sheet information in define1-0-0.xsl is not guaranteed to work for all
browser types and versions to produce the correct HTML, but it does work for
Internet Explorer 6.0 and higher.
5 Ensure that the first few rows of the first table appear similar to this image:
Note: Minor variations in appearance are possible and are not a problem.
Reviewing these rows is sufficient to confirm that the product is installed and
functioning properly.
6 Ensure that the define.xml file contains tables for the following:
n
For each domain, a table that lists the domain’s variables.
n
Computational Algorithms Section
Steps 57
n
Controlled Terminology
7 In the last table in define.xml (which contains controlled terminology), ensure that the
last few items in the file are values for VSTESTCD, including the values BMI and
WEIGHT.
8 Close the SAS session.
58 Chapter 11 / Test 5: Create Define.xml
Sign-Off
Test 5: Create Define.xml
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
59
Part 5
SDTM
Chapter 12
Test 1: Validate SDTM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Chapter 13
Test 2: Build Source Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Chapter 14
Test 3: Build Source Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Chapter 15
Test 4: Build SAS Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Chapter 16
Test 5: Report Check Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
60
61
12
Test 1: Validate SDTM
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Introduction
This test runs the sample program that is provided as part of the SDTM 3.1.3 standard.
If this program runs successfully and produces the expected results, the SDTM 3.1.3
standard is correctly installed and functioning properly.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_SDTM/programs/validate_data.sas.
3 Select Run  Submit.
The program outputs to the SAS log and generates a validation_results data set and
a validation_metrics data set.
62 Chapter 12 / Test 1: Validate SDTM
TIP In the SAS Explorer, you can view these data sets in the Results library.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the validation_results data set to ensure that the following conditions are
met:
n
For the records where the column labeled Validation check identifier (named
checkid) is blank, examine the message column to ensure that paths and
process metadata are correct.
n
The column labeled Process status (named _cst_rc) is 0 for all records. There
are not any checks with the result severity = 'Warning: Check not run'.
n
The data set contains 312 records.
6 Review the validation_metrics data set and ensure that it contains these last few
rows:
Metric Parameter
# of distinct check invocations
Count of Records
15
# check invocations not run
1
Errors (severity=High) reported
1
Warnings (severity=Medium) reported
Notes (severity=Low) reported
Structural errors, warnings and notes
Content errors, warnings and notes
7 Close the SAS session.
91
118
0
210
Sign-Off 63
Sign-Off
Test 1: Validate SDTM
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
64 Chapter 12 / Test 1: Validate SDTM
65
13
Test 2: Build Source Data
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Introduction
This test references derived data from a CRT-DDS (define.xml) file to build a library of
SDTM 3.1.3 domains.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_SDTM/programs/create_sasdatafromxpt.
3 Select Run  Submit.
The code outputs to the SAS log and creates an xpt_results data set in the
CST_SDTM/results directory and 36 data sets in the CST_SDTM/derived/data
directory.
66 Chapter 13 / Test 2: Build Source Data
Note: For this program, the library information was cleaned up, so these files are
not immediately accessible under Libraries in the SAS Explorer. On Microsoft
Windows, you can access these files through the SAS Explorer by navigating from
within the SAS Explorer starting at the node labeled My Computer. On UNIX, it is
necessary for you to copy these data sets into a directory that is viewable by the
SAS Explorer (for example, your Home Directory listed under Favorite Folders).
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
You might sporadically see warnings in the SAS log such as WARNING: Libname
<libref> is not assigned. These occur with redundant requests to clear
SAS librefs or filerefs and do not indicate a problem with the SAS Clinical Standards
Toolkit installation.
5 Review the xpt_results data set to ensure that the following conditions are met:
n
The Resolved message text from message file column (named message)
contains correct paths and process metadata.
n
The column labeled Process status (named _cst_rc) is 0 for all records. There
are not any checks with resultseverity=’Warning: Check not run’.
Steps 67
n
The data set contains 18 records and that a record near the end reports Process
completed successfully.
See the sample output above.
Note: Values that refer to temporary directories, files, or PROCESS DATE: vary.
6 Review the CST_SDTM/derived/data directory to ensure that the following
conditions are met:
n
There are 36 new SAS data sets.
n
The dm data set has 70 records and 28 columns.
7 Close the SAS session.
68 Chapter 13 / Test 2: Build Source Data
Sign-Off
Test 2: Build Source Data
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
69
14
Test 3: Build Source Metadata
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Introduction
This test references derived data from a CRT-DDS (define.xml) file to build a set of
SDTM 3.1.3 metadata in a structure required by the SAS Clinical Standards Toolkit.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_SDTM/programs/create_sourcemetadata.sas.
3 Select Run  Submit.
This program outputs to the SAS log and creates data sets in both the results and
derived/metadata subdirectories in the CST_SDTM directory.
70 Chapter 14 / Test 3: Build Source Metadata
Note: For this program, the library information was cleaned up, so these files are
not immediately accessible under Libraries in the SAS Explorer. On Microsoft
Windows, you can access these files through the SAS Explorer by navigating from
within the SAS Explorer starting at the node labeled My Computer. On UNIX, it is
necessary for you to copy these data sets into a directory that is viewable by the
SAS Explorer (for example, your Home Directory listed under Favorite Folders).
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the srcmeta_results data set in the CST_SDTM/results directory to ensure
that the following conditions are met:
n
The Resolved message text from message file column (named message)
contains correct paths and process metadata.
n
Ensure that the column labeled Process status (named _cst_rc) is 0 for all
records.
Steps 71
n
Ensure that the data set contains 28 records.
See the sample output above.
Note: Values that refer to temporary directories, files, or PROCESS DATE: vary.
n
Where the Result identifier equals CST0074, the records report that study
reference data was created in folder CST_SDTM/derived/metadata.
72 Chapter 14 / Test 3: Build Source Metadata
6 Review the CST_SDTM/derived/metadata directory to ensure that the following
conditions are met:
n
There are five new data sets: source_columns, source_study,
source_documents, source_values, and source_tables.
n
The source_tables data set has 36 records and 15 columns.
7 Close the SAS session.
Sign-Off 73
Sign-Off
Test 3: Build Source Metadata
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
74 Chapter 14 / Test 3: Build Source Metadata
75
15
Test 4: Build SAS Formats
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Introduction
This test references derived data from a CRT-DDS (define.xml) file to build a SAS
format catalog representing the codelists in the CRT-DDS file.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_SDTM/programs/create_formatsfromcrtdds.sas.
3 Select Run  Submit.
The code outputs to the SAS log and creates a codelist_results data set in the
CST_SDTM/results directory and creates a catalog named cterms in the
CST_SDTM/derived/formats directory.
76 Chapter 15 / Test 4: Build SAS Formats
Note: For this program, the library information was cleaned up, so these files are
not immediately accessible under Libraries in the SAS Explorer. On Microsoft
Windows, you can access these files through the SAS Explorer by navigating from
within the SAS Explorer starting at the node labeled My Computer. On UNIX, it is
necessary for you to copy these data sets into a directory that is viewable by the
SAS Explorer (for example, your Home Directory listed under Favorite Folders).
At the end of the run, the FMTLIB output appears.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the codelist_results data set in the CST_SDTM/results directory to ensure
that the following conditions are met:
n
The Resolved message text from message file column (named message)
contains correct paths and process metadata.
n
The column labeled Process status (named _cst_rc) is 0 for all records. There
are not any checks with the result severity='Warning: Check not run'.
n
The data set contains 18 records. One of the last records must report Process
completed successfully.
See the sample output above.
Sign-Off 77
Note: Values that refer to temporary directories, files, or PROCESS DATE: vary.
6 Ensure that the CST_SDTM/derived/formats directory contains a cterms catalog
(named cterms.sas7bcat).
7 Open the cterms catalog and verify that it has 53 formats.
Note: The data set can show a different number of formats if it previously existed. In
this case, the 53 formats are appended to the file.
8 Close the SAS session.
Sign-Off
Test 4: Build SAS Formats
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
78 Chapter 15 / Test 4: Build SAS Formats
79
16
Test 5: Report Check Metadata
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Introduction
This test verifies that all metadata about SDTM 3.1.3 validation checks is properly
installed. A sample report itemizes this metadata.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_SDTM/programs/cst_metadatareport.sas.
3 Select Run  Submit.
This program outputs to the SAS log and generates a PDF file named
cstcheckmetadatareport.pdf in the CST_SDTM/results directory.
Note: No result data set is created.
80 Chapter 16 / Test 5: Report Check Metadata
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the PDF file.
a Ensure that all four of these report sections were generated:
n
The Report Procedure (Check Overview)
n
Additional Check Details
n
Message Details
n
Reference Information
b Ensure that all titles, footnotes, column headings, and cell contents appear
correct.
c In the Reference Information section, look for at least one value of OpenCDISC in
the column named Source of Information (for example, the row for validation
check SDTM0231).
6 Close the SAS session.
Sign-Off 81
Sign-Off
Test 5: Report Check Metadata
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
82 Chapter 16 / Test 5: Report Check Metadata
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